Photonic crystal microarray device for label-free multiple analyte sensing, biosensing and diagnostic assay chips

ABSTRACT

Methods and systems for label-free multiple analyte sensing, biosensing and diagnostic assay chips consisting of an array of photonic crystal microcavities along a single photonic crystal waveguide are disclosed. The invention comprises an on-chip integrated microarray device that enables detection and identification of multiple species to be performed simultaneously using optical techniques leading to a high throughput device for chemical sensing, biosensing and medical diagnostics. Other embodiments are described and claimed.

BACKGROUND OF THE INVENTION

1. Field of the Invention

This invention relates generally to the field of optical and medicaldevices, and more specifically to an apparatus and method for microarrayimplementation for the detection of multiple analytes such as chemicalagents and biological molecules using photonic crystals.

2. Background of the Invention

Label-free optical sensors based on photonic crystals have beendemonstrated as a highly sensitive potential method for performing alarge range of biochemical and cell-based assays. For backgroundinformation on photonic crystals, the reader is directed toJoannopoulos, J. D., R. D. Meade, and J. N. Winn, Photonic Crystals,1995 Princeton, N.J.: Princeton University Press. Tight confinement ofthe optical field in photonic crystal microcavities leads to a stronginteraction with the surrounding ambient in the vicinity of themicrocavity, thereby leading to large sensitivity to changes inrefractive index of the ambient. Much of the research in photoniccrystal devices has relied on enhancing refractive index sensitivity toa single analyte (Lee M. R., Fauchet M., “Nanoscale microcavity sensorfor single particle detection,” Optics Letters 32, 3284 (2007).).Research on photonic crystals for multiple analyte sensing has focusedon one-dimensional photonic crystal grating-like structures (see patentsUS20080225293 and US20030027328), that measure the resonant peakreflected wavelengths; such sensors have wide linewidths of the resonantpeaks due to one-dimensional confinement and do not utilize the fullpotential of narrow resonant linewidths of two-dimensional photoniccrystal microcavities. Furthermore, measurements are made from eachsensor element in the array in a serial process, requiring multiplesources and detectors for parallel sensing beyond a single element.Research has been performed with one-dimensional photonic crystalmicrocavities coupled to ridge waveguides (See Mandal S, and Erickson D,“Nanoscale optofluidic sensor arrays”, Optics Express 16, 1623 (2008)).One dimensional photonic crystal microcavities, in addition to pooroptical confinement, do not utilize the slow light effect due to reducedgroup velocity in two-dimensional photonic crystal waveguides that wouldotherwise enhance coupling efficiency and thereby improvesignal-to-noise ratio of sensing. Two dimensional photonic crystalwaveguide biosensors demonstrated rely on shifts of the stop-gap (seeSkivesen N. et al, “Photonic crystal waveguide biosensor”, OpticsExpress 15, 3169 (2007)) or shifts of the resonant peak of an isolatedmicrocavity (see Chakravarty S et al, “Ion detection with photoniccrystal microcavities”, Optics Letters 30, 2578 (2005).). In eithercase, the design is not suitable for the fabrication of microarrays formultiple analyte sensing.

Two dimensional photonic crystal microcavities integrated withtwo-dimensional photonic crystal waveguides offer the possibility ofintegrating the high quality-factor resonances of two-dimensionalphotonic crystal microcavities with the slow light effect oftwo-dimensional photonic crystal waveguides for high sensitivity, highsignal-to-noise ratio sensing. Furthermore, multiple photonic crystalmicrocavities can be simultaneously arrayed along a single photoniccrystal waveguide, so that a single measurement can be performed inparallel to elicit the response from multiple sensor elements, therebyincreasing measurement throughput and reducing cost. An array of twosensors demonstrated using two-dimensional photonic crystalmicrocavities uses multiple ridge waveguides between individual photoniccrystal microcavities. Coupling between photonic crystal waveguides andridge waveguides introduces additional significant transmission loss ateach interface, thereby significantly reducing signal-to-noise ratio aseach microcavity is added for multiple sensing. The design demonstratedby Guillermain et al (see Guillermain E, Fauchet P. M., “Multi-channelsensing with resonant microcavities coupled to a photonic crystalwaveguide,” JWA 45, CLEO Conference (2009)) in effect employs multiplephotonic crystal waveguides and also employs microcavities withsignificantly poor quality factors that make the designs unsuitable forhigh sensitivity sensing. Better designs are needed in the art torealize photonic crystal microarray devices that efficiently couplelight from ridge waveguides to a single photonic crystal waveguide,wherein multiple photonic crystal microcavities with high qualityfactors and covering a large bandwidth for sensing are coupled to asingle photonic crystal waveguide for high sensitivity multiple sensing.

A standard on-chip multiple protein patterning technique usinglithography typically requires a pre-bake resist temperature of 100° C.or higher. At the very least, temperatures this high compromise or alterbiological functionality, and at the very worst they may destroy itsfunction. Most proteins are stable in vivo at a temperature of 37° C.,but this stability is dependent on chaperone proteins that maintain theproper conformation of other proteins in cells. Since proteins in vitrolack these chaperone proteins, they must be maintained at even lowertemperatures to prevent denaturation and loss of function. Designs areneeded to enable patterning of different kinds of biomolecules inaqueous phase to preserve functionality of biomolecules.

Designs are needed in the art to integrate two-dimensional photoniccrystal microcavities with two-dimensional photonic crystal waveguidesfor multiple analyte sensing and designs are further needed to patternmultiple biomolecules, of different constitutions, on the photoniccrystal substrate while preserving their functionality.

SUMMARY OF THE INVENTION

One embodiment of the invention provides a sensor comprising asemiconductor material core with high dielectric constant, supported onthe bottom by a low dielectric constant cladding. A triangular latticeof photonic crystal holes is etched into the substrate. Photonic crystalwaveguide is defined by filling a single row of holes, from input ridgewaveguide transition to output ridge waveguide transition with thesemiconductor core material. Photonic crystal microcavity is similarlydefined by filing a few holes with semiconductor core material. Multiplephotonic crystal microcavities are patterned at a distance of threelattice constants from the photonic crystal waveguide. The distancebetween individual photonic crystal microcavities is 10 lattice periods.The high dielectric constant core with structured photonic crystalwaveguide and photonic crystal microcavities, together with the lowdielectric constant cladding, form the photonic crystal microarraystructure. Light is coupled into the photonic crystal waveguide from aridge waveguide. Light is out-coupled from the photonic crystalwaveguide to an output ridge waveguide. When a broadband light source isinput to the photonic crystal waveguide, wavelengths corresponding tothe resonant wavelengths of the individual microcavities are coupled tothe corresponding microcavities. As a result, minima are observed in thetransmission spectrum corresponding to the dropped wavelength of eachphotonic crystal microcavity. Depending upon the wavelength range ofinterrogation, the period of the sub-wavelength lattice can vary from 50nm to 1500 nm and the depth of the lattice structure can vary from 0.4to 0.7 times the lattice periodicity above. The semiconductor materialcan be silicon (or any Group IV material), gallium arsenide (or anyIII-V semiconductor) or any semiconductor material with high refractiveindex. The substrate can be any Group IV material corresponding to theGroup IV core material, or any substrate suitable to grow the III-V corematerial. Above the microcavity, a thin film of target binding moleculesthat are immobilized on the microcavity surfaces, each microcavitysurface being coated with an exclusive target molecule or biomolecule,forms the dielectric coating. The one or more binding molecules are freeof detection labels. The one or more specific binding substances arethus arranged in an array on the microcavities, along the photoniccrystal waveguide. A single transmission spectrum therefore probes thebinding events on multiple microcavities. A binding event on a specificmicrocavity shifts the corresponding transmission minimum and leads to asensing event for the specific microcavity. Analyzed biomolecules can beproteins, DNA, RNA, small molecules or genes. Arrays of microcavitiestherefore lead to a multiple analyte sensing device that increases themeasurement throughput of the device, in addition to the obvioussensitivity enhancements achieved by using two-dimensional photoniccrystal waveguide coupled to two-dimensional photonic crystalmicrocavities.

To summarize:

The primary objective of the invention is to provide an integratedphotonic crystal microarray with compact size that can be monolithicallyintegrated with different kinds of biomolecules such as proteins,nucleic acids, DNA, RNA or small molecules to implement a personalizeddiagnostic chip.

The second objective of the invention is to eliminate the need forlabeling of biomolecule and biomolecule conjugates for on-chip detectionand thereby reduce microarray costs associated with biomoleculelabeling.

The third objective of the invention is to significantly increasemeasurement throughput from devices by signal collection and analysisfrom multiple elements of a microarray in a single measurement asopposed to individual element measurement in contemporary systems.

The fourth objective of the invention is to implement a novellithography scheme on a CMOS chip that avoids high temperature processesassociated with photolithography and chemical etching for the patterningof multiple biomolecules and thereby preserves biomolecule functionalityin aqueous phase at room temperatures or even colder if necessary.

Other objectives and advantages of the present invention will becomeapparent from the following descriptions, taken in connection with theaccompanying drawings, wherein, by way of illustration and example, anembodiment of the present invention is disclosed.

BRIEF DESCRIPTION OF THE DRAWINGS

The drawings constitute a part of this specification and includeexemplary embodiments of the present invention, which may be embodied invarious forms. It is to be understood that in some instances variousaspects of the present invention may be shown exaggerated or enlarged tofacilitate an understanding of the invention.

A more complete and thorough understanding of the present invention andbenefits thereof may be acquired by referring to the followingdescription together with the accompanying drawings, in which likereference numbers indicate like features, and wherein:

FIG. 1A is a top view of one embodiment of a photonic crystal microarraydevice based on an array of N photonic crystal microcavities coupled toa photonic crystal waveguide. In FIG. 1A, N is chosen arbitrarily as 4for space constraints. FIG. 1B is an enlarged section of FIG. 1A.

FIG. 2 is a cross-sectional view of the device shown in FIG. 1B takenalong line A-A′.

FIG. 3 is a top view of one embodiment of a photonic crystal microarraydevice based on an array of N photonic crystal microcavities coupled toa photonic crystal waveguide where each photonic crystal microcavity iscoated with a different biomolecule.

FIG. 4 is a top view of the field intensity pattern of a guided mode ofa photonic crystal waveguide depicted in FIG. 1B taken along line A-A′.

FIG. 5 is a top view of the field intensity pattern of a photoniccrystal microcavity defect mode for the linear microcavity depicted inFIG. 1B taken along line B-B′.

FIG. 6 illustrates a typical diagram of the dispersion relation of aphotonic crystal waveguide and individual microcavities with resonantmodes in the low dispersion low group velocity region for enhanced modecoupling from waveguide to microcavity.

FIG. 7A shows a top view of a functional photonic crystal waveguide withtwo representatively coupled photonic crystal microcavities along thelength of the photonic crystal waveguide. Two (2) microcavities arechosen, as a representative number for n. n can vary from 1 to N (N→∞).FIG. 7B shows the transmission spectrum of the embodiment depicted inFIG. 7A.

FIG. 8A shows a top view of a functional photonic crystal microcavity.Elements that are geometrically tuned in size and/or position areindicated. FIG. 8B shows the transmission spectrum when tworepresentative photonic crystal microcavities of the embodiment depictedin FIG. 8A are coupled to the functional photonic crystal waveguide inFIG. 1A and FIG. 1B. It is shown that geometry tuning can shift resonantfrequencies and optimum spacing between microcavities ensures nocross-talk between adjacent microcavities.

FIG. 9 shows another transmission spectrum of a functional photoniccrystal waveguide with two representatively coupled photonic crystalmicrocavities of the embodiment depicted in FIG. 8A along the length ofthe functional photonic crystal waveguide in FIG. 1A and FIG. 1B. Two(2) microcavities are chosen, as a representative number for n. n canvary from 1 to N (N→∞). It is shown that geometry tuning can shiftresonant frequencies and thereby allows the potential to couple Nphotonic crystal microcavities in an array, each with a small differencein geometry, hence a small difference in resonant frequency and hencepotential of the device to respond to multiple analytes, molecules andbiomolecules.

FIG. 10A through FIG. 10I shows the steps in the fabrication ofmicrofluidic channels on patterned silicon chips for biomoleculedelivery and subsequent removal to create arrays of biomolecule coatedphotonic crystal microcavities.

FIG. 11 is a top view of the device in FIG. 10G and FIG. 10H.

DETAILED DESCRIPTIONS OF THE PREFERRED EMBODIMENTS Detailed Descriptionof the Invention

In accordance with a preferred embodiment of the present invention, adevice for a microarray for personalized diagnostic applicationscomprises: a functional photonic crystal waveguide having a waveguidecore along which light is guided, arrays of photonic crystalmicrocavities along the length of the photonic crystal waveguide eachcoated with a separate biomolecule specific to disease identification,an input and output photonic crystal waveguide with gradually changedgroup index before and after the functional photonic crystal waveguide,which can bridge the refractive indices difference between conventionaloptical waveguides and the functional photonic crystal waveguide. Thesensor can be used to detect organic or inorganic substances such asproteins, DNA, RNA, small molecules, nucleic acids, virus, bacteria,cells, genes, without requiring labels such as fluorescence orradiometry. Light (from a broadband source or LED) coupled into aphotonic crystal waveguide couples with the resonance of a photoniccrystal microcavity and thereby drops the resonant wavelength in themicrocavity, leading to a minimum in the transmission spectrum of thephotonic crystal waveguide at the resonant wavelength. Transmissionminima are observed for each resonant wavelength of the individualmicrocavities along the photonic crystal waveguide. The resonancewavelength shifts to longer wavelengths in response to the attachment ofa material on the microcavity surface leading to the corresponding shiftof the transmission minimum of that microcavity.

In another embodiment of the present invention, a device for amicroarray for multiple analyte sensing applications comprises: afunctional photonic crystal waveguide having a waveguide core alongwhich light is guided, arrays of photonic crystal microcavities alongthe length of the photonic crystal waveguide each coated with a separatepolymer or hydrogel specific to a unique environmental parameter, aninput and output photonic crystal waveguide with gradually changed groupindex before and after the functional photonic crystal waveguide, whichcan bridge the refractive indices difference between conventionaloptical waveguides and the functional photonic crystal waveguide. Thesensor can be used to detect changes in temperature, pressure, humidity,molarity of solution, acidity or alkalinity (pH) of aqueous medium, ionconcentration of solutions, trace gases in the atmosphere, pollutants inground water that can be organic or inorganic, volatile andnon-volatile, pesticides and thereof in a single optical transmissionmeasurement. A unique polymer or hydrogel is chosen with maximumresponse to changes in each of the above parameters and a uniquemicrocavity along the waveguide is coated with a unique polymer orhydrogel. Light (from a broadband source or LED) coupled into a photoniccrystal waveguide couples with the resonance of a photonic crystalmicrocavity and thereby drops the resonant wavelength in themicrocavity, leading to a minimum in the transmission spectrum of thephotonic crystal waveguide at the resonant wavelength. Transmissionminima are observed for each resonant wavelength of the individualmicrocavities along the photonic crystal waveguide, in the pristinecondition. The resonance wavelength shifts to longer wavelengths inresponse to changes in ambient parameters listed above leading to thecorresponding shift of the transmission minimum of that microcavity, theamount of transmission minimum shift determines the absolute change inambient conditions in the vicinity of the microarray device.

For the measurement of environmental parameters in situ, the device isincorporated with a filter to remove macroscopic dirt and dustparticles. The filter can be a macroscopic filter incorporated off-chipor a microfluidic filter incorporated on-chip.

Methods for fabricating photonic crystal structures are widely describedin the literature. Sensor structures of the invention have highersensitivity than previous structures due to the use of two-dimensionalphotonic crystal microcavities with resonances that have high qualityfactor together with the slow light effect of two-dimensional photoniccrystal waveguides. Methods for patterning of multiple biomoleculesexclusively on photonic crystal microcavities that preserves biomoleculefunctionality in aqueous phase are disclosed. The amount of refractiveindex change and hence the shift in resonance frequency is determined bythe amount of adsorbed molecules or biomolecules on the microcavitysurface that interacts with the electromagnetic field of the photoniccrystal. The system is capable of detecting a single cell attached toits surface.

Microarrays provide an unprecedented opportunity for comprehensiveconcurrent analysis of thousands of biomolecules such as proteins,genes, DNA molecules, small molecules or nucleic acids. The globalanalysis of the response to a toxic agent, as opposed to the historicalmethod of examining a few select biomolecules, provides a more completepicture of toxicologically significant events. Array-based expressionprofiling is useful for differentiating compounds that interact directlywith the species from those compounds that are toxic via a secondarymechanism. Microarrays are consequently finding numerous applications inpathogen detection and biodefense. The sensors have utility in thefields of pharmaceutical research (e.g., high throughput screening,secondary screening, quality control, cytoxicity, clinical trialevaluation), life science research (e.g., proteomics, proteininteraction analysis, DNA-protein interaction analysis, enzyme-substrateinteraction analysis, cell-protein interaction analysis), diagnostictests (e.g., protein presence, cell identification), environmentaldetection (bacterial and spore detection and identification), andbio-warfare defense.

The principles of the invention can also be applied to e.g., evanescentwave based biosensors and any biosensors incorporating an opticalwaveguide. The principle can also be applied to arrays of ring or diskresonators coupled to a bus waveguide. However such waveguides providelimited free-spectral range for microcavity resonances and also do notincorporate slow light effect of photonic crystal waveguides and arethus less sensitive with low signal-to-noise ratio.

Detailed descriptions of the preferred embodiments are provided herein.It is to be understood, however, that the present invention may beembodied in various forms. Therefore, specific details disclosed hereinare not to be interpreted as limiting, but rather as a basis for theclaims and as representative basis for teaching one skilled in the artto employ the present invention in virtually any appropriately detailedsystem, structure or manner.

Defect engineered photonic crystals, with sub-micron dimensions havealready demonstrated high sensitivity to trace volumes of analytes.While biosensing has been demonstrated in photonic crystal devices withsingle biomolecules, no previous effort has been made to extend thedevice capability to microarrays. Particularly, patterning of multiplebiomolecules on a few micron scales has faced challenges of bindingexclusivity and binding specificity. Our proposed device consists of anarray of photonic crystal microcavity resonators coupled to a singlephotonic crystal waveguide that give rise to minima in the photoniccrystal waveguide transmission spectrum at the resonance frequency ofthe microcavity. Using a new microfluidic technique, individual targetbiomolecules are coated exclusively on individual photonic crystalmicrocavities. Our method eliminates labeling for analyteidentification. The impact of our novel and robust multi-analyte sensingtechnique can reach much further than the field of biomolecular scienceand diagnostics alone. This section will provide detailed description ofthe preferred embodiments in the aspect of device architecture, as wellas the design concept and working principle.

FIG. 1A presents a schematic drawing of a photonic crystal microarray.It consists of a functional photonic crystal waveguide 100, input ridgewaveguide 112, output ridge waveguide 113 and an array of N photoniccrystal microcavities 20 n where n represents digits and ranges from 1to N (N→∞). The functional photonic crystal waveguide 100 includes anumber of column members 102 etched through or partially into thesemiconductor slab 101. The waveguide core 141 is defined as the spacebetween the centers of two column members adjacent to the region wherethe columns are absent. In one preferred embodiment, the column members102 are arranged to form a periodic lattice with a lattice constant α.In some embodiments, the width of waveguide core 141 can range fromsqrt(3)/2 to 50 sqrt(3). The arrows indicate the direction in whichelectromagnetic waves are coupled into and out of the photonic crystalwaveguide respectively. In the figure, due to space limitations, themicrocavities are designated as 201, 202, . . . , 20(n−1) and 20 nrespectively. The photonic crystal microcavities are parallel to thephotonic crystal waveguide and are placed 3 lattice periods away fromthe waveguide. FIG. 1B is an enlarged section of FIG. 1A showing thephotonic crystal microcavity elements 201, 202, columnar members 102,and photonic crystal waveguide 100 in greater detail. The photoniccrystal waveguide 100 is defined by filling a complete row of columnarmembers with the semiconductor slab material 101. Similarly, a photoniccrystal microcavity, for instance 201, is defined by filing a row of 4columnar members 102 with semiconductor material 101. The distancebetween individual photonic crystal microcavities is 12 periods. Oneskilled in the art will notice that the photonic crystal microcavity 201can have different geometries as described in the literature. Theresonant wavelength of a photonic crystal microcavity is dependent onthe geometry of the microcavity. Light propagating in a photonic crystalwaveguide couples to a photonic crystal microcavity at the resonantwavelength of the microcavity. The transmission spectrum of the photoniccrystal waveguides consequently shows minima corresponding to theresonant wavelength of each photonic crystal microcavity. With referenceto FIG. 2, which is a cross-sectional view of the functional photoniccrystal waveguide 100 in FIG. 1 taken along line A-A′, the columnmembers 102 extend throughout the thickness of the slab 101 to reach abottom cladding 105. In one embodiment, the top cladding 106 is air.However, one skilled in the art will note that the top cladding can beany organic or inorganic dielectric material, columnar members 102 canextend through both 106 and 101 as well as through the bottom cladding105 to reach the substrate 107. Although the structure within the slab101 is substantially uniform in the vertical direction in thisembodiment, one skilled in the art will understand that verticallynon-uniform structure, such as the columnar members 102 whose radii arevarying along the vertical direction, may be used as well. The columnmembers 102 can be either simply void or filled with other dielectricmaterials. Between the ridge waveguide 112 and the core photonic crystalwaveguide 100, there is an impedance taper 115 for coupling of lightfrom ridge waveguide to photonic crystal waveguide with high efficiency.Similarly, at the output, between the photonic crystal waveguide 100 andthe output ridge waveguide 113, there is another impedance taper 114 forbetter coupling efficiency. The waveguides are tapered by shifting thecolumnar members by x times α in the direction perpendicular to 100, inthe plane of the waveguide, where α is the lattice constant and x variesfrom 0.05 to 0.4 in steps of 0.05, from photonic crystal waveguide toridge waveguide. For a photonic crystal waveguide 100, 114 and 115,which comprise photonic crystals of two-dimensional periodicity, thewave guiding in the vertical direction must be provided by conventionalindex-guiding scheme. This means a substrate 105 and a superstrate 106with a lower effective index relative to that of the slab material mustbe disposed below and above the slab 101. In FIG. 2, the superstrate isabsent and simply represented by air or vacuum. On one side, thesubstrate 105 and superstrate 106 prevent guided lightwave escaping faraway from the top and bottom surfaces of the slab 101. In mostapplications, it is desirable that the waveguide have a single guidedmode, which can be achieved through adjusting the width of the waveguidecore 141.

In FIG. 3, substances are coated on the photonic crystal microcavity arelabeled as 301, 302, . . . , 30(n−1), 30 n, where n represents digitsand ranges from 1 to N (N→∞). Each photonic crystal microcavity 20 n iscoated with a specific substance 30 n. In one embodiment, the substancecan be a biomolecule such as proteins, nucleic acids, DNA, RNA,antigens, antibodies, small molecules, peptides, genes etc. Eachbiomolecule can be specific to a particular disease causing conjugatewhere the disease of interest can be cancer, malaria, Leptospirosis orany infectious disease to achieve specific detection. In anotherembodiment, the substance 30 n can be a hydrogel that swells in thepresence of a specific analytical solution or ambient gas wherein theambient gas includes, but is not limited to, greenhouse gases such ascarbon dioxide, methane, nitrous oxide or other gases such as oxygen,nitrogen thereof. In yet another embodiment, the substance can be apolymer that changes its effective refractive index upon contact with achemical substance or proportionately to changes in temperature,humidity and pressure thereof. The device is therefore a verygeneralized construction where multiple polymer or biological molecules,each specific to detection of a specific species, are arrayed forsimultaneous detection.

FIG. 4 depicts a top view of the field intensity pattern of a guidedmode of a waveguide 100 in FIG. 1 and FIG. 3. The circles indicatecolumnar members of the photonic crystal waveguide. It is seen in FIG. 4that peak of the field intensity is well confined inside the waveguidecore region 141. Outside of 141, there are two side peaks due toevanescent field. Due to even symmetry of the mode with respect to thecenter of the waveguide, the mode couples very well with resonant modesof photonic crystal microcavities which possess even symmetry.

FIG. 5 depicts a top view of the field intensity pattern of a defectmode of a photonic crystal microcavity 20 n where n represents digitsand ranges from 1 to N (N→∞), in FIG. 1 and FIG. 2. The circles indicatecolumnar members of the photonic crystal microcavity. It is seen in FIG.5 that peak of the field intensity is well confined inside the photoniccrystal microcavity region 151. Outside of 151, there is very weak fieldintensity that overlaps with the columnar members. FIG. 5 suggests thatphotonic crystal microcavity resonant mode is well confined in thedielectric, in the plane of the waveguide inside region 151.

The bold curve 190 in FIG. 6 depicts a dispersion diagram of thephotonic crystal waveguide 100. Three regions are distinctly visible inthe bold curve. A region 161 where dω/dk is almost zero, a region 163where dω/dk is very high and a region 162 where dω/dk has intermediatevalues. dω/dk denotes the group velocity of light propagating in thephotonic crystal waveguide at the corresponding frequency. The region164 denotes the stopgap of the photonic crystal waveguide where thetransmission is zero. The coupling efficiency between a photonic crystalwaveguide and a photonic crystal microcavity is inversely proportionalto the group velocity, consequently slower the group velocities higherthe coupling due to higher interaction time. However, region 161 is notsuitable due to high dispersion and consequently high transmission loss.We identify a range of frequencies in region 162 between dotted lines191 and 192 over which we vary the resonance of the photonic crystalmicrocavity to achieve high coupling efficiency with photonic crystalwaveguide 100.

FIG. 7, FIG. 8, FIG. 9 address photonic crystal microcavity designissues so that the entire range of frequencies between the dotted lines191 and 192 can be efficiently used for resonant coupling, therebyincreasing the number of microcavities that be arrayed in parallel forthe multiple analyte sensing diagnostic chip. FIG. 7A depicts oneembodiment of a photonic crystal microcavity where a row of 4 columnarmembers 102 has been filled with the semiconductor dielectric material101. We consider a photonic crystal waveguide transmission spectrum when2 photonic crystal microcavities say 201 and 202 in FIG. 1 are coupledto the photonic crystal waveguide 100. For the microcavity 201, thecolumnar members 501 and 502, have been shifted by −0.2α and formicrocavity 202 the columnar members 503 and 504 are shifted by +0.2α,where α denotes the lattice periodicity of the triangular latticephotonic crystal structure. In FIG. 7B, 2 sharp minima 511 and 512 areobserved that correspond to the resonance of corresponding photoniccrystal microcavities 201 and 202. This demonstrates that progressivegeometry tuning of photonic crystal microcavities can result in multiplemicrocavities arrayed along a photonic crystal waveguide, each with aunique resonance frequency resulting in a unique transmission minimum inthe photonic crystal waveguide 100 transmission spectrum.

FIG. 8A depicts another embodiment of a photonic crystal microcavitywhere a row of 4 columnar members 102 has been filled with thesemiconductor dielectric material 101. We consider a photonic crystalwaveguide transmission spectrum when 2 photonic crystal microcavitiessay 201 and 202 in FIG. 7A are coupled to the photonic crystal waveguide100. As in FIG. 7A, for the microcavity 201, the columnar members 501and 502, have been shifted by −0.2α in the Γ-K direction and formicrocavity 202 the columnar members 503 and 504 are shifted by +0.2α inthe Γ-K direction, where α denotes the lattice periodicity of thetriangular lattice photonic crystal structure. For the microcavity 202,as illustrated in general for a microcavity 20 n, the diameters of themembers 601-610 are further reduced in size to 0.9 times the diameter ofcolumnar members 102 elsewhere. Two sharp minima 513 and 514 areobserved that correspond respectively to the resonance of correspondingphotonic crystal microcavities 201 and 202. The transmission minimum 514is red-shifted corresponding to the transmission minimum 512 in FIG. 7B.The transmission minimum 513 is not shifted corresponding to thetransmission minimum 511 in FIG. 7B since the geometry of microcavity201 has not been changed from FIG. 7A. The fact is significant sincethis ensures that our design selection of 12 lattice periods betweenadjacent microcavities is optimum and does not alter either a resonancequality factor or the resonance wavelength of a designed microcavity. Byreducing the diameter of the columnar members 601-610, the dielectricfraction inside the resonant mode of 202 is increased which brings thefrequency of the mode down, closer to the dotted line 192 in FIG. 6. Thediameter of the columnar members 601-610 can thus be changed in step toachieve a new microcavity design with a different resonant frequency.

FIG. 9A depicts another embodiment of a photonic crystal microcavitywhere a row of 4 columnar members 102 has been filled with thesemiconductor dielectric material 101. We consider a photonic crystalwaveguide transmission spectrum when 2 photonic crystal microcavitiessay 201 and 202 in FIG. 7A are coupled to the photonic crystal waveguide100. For the microcavity 201, the columnar members 501 and 502, havebeen shifted by −0.2α and for microcavity 202 the columnar members 503and 504 are shifted by +0.2α, where a denotes the lattice periodicity ofthe triangular lattice photonic crystal structure. For the microcavity202, the diameters of the members 601-610 are reduced in size to 0.9times the diameter of columnar members 102 elsewhere. For themicrocavity 201, the diameters of the members 601-610 are increased insize to 1.05 times the diameter of columnar members 102 elsewhere. Twosharp minima 515 and 516 are observed that correspond respectively tothe resonance of corresponding photonic crystal microcavities 201 and202. The transmission minimum 515 is blue-shifted corresponding to thetransmission minimum 511 in FIG. 7B. The transmission minimum 516 isred-shifted corresponding to the transmission minimum 514 in FIG. 8B andred-shifted further corresponding to the transmission minimum 512 inFIG. 7B. By further reducing the diameter of the columnar members601-610 compared to FIG. 8B, the dielectric fraction inside the resonantmode of 202 is further increased which brings the frequency of the modedown further, and even closer to the dotted line 192 in FIG. 6. Byincreasing the diameter of the columnar members 601-610, the dielectricfraction inside the resonant mode of 201 is decreased, which raises thefrequency of the resonant mode, closer to the dotted line 191 in FIG. 6.The diameter of the columnar members 601-610 can thus be changed insteps to achieve a new microcavity design with a different resonantfrequency.

The second design concept of this invention is depicted in FIG. 10 thatconcerns the patterning of biomolecules onto the patterned siliconsubstrate 411 using a novel microfluidic technique that preservesbiomolecule functionality in aqueous phase at all times. In oneembodiment, biomolecules are patterned on a photonic crystal patternedsilicon substrate with a thin layer of silicon dioxide. The thickness ofsilicon dioxide is not more than 10 nanometers. FIG. 10 shows the stepsin the fabrication process on a patterned substrate that preserves thebiomolecule functionality in aqueous phase. A film, 412 is deposited onthe substrate in FIG. 10A. In one embodiment, the film 412 is parylene.A thin film of metal 413 is sputtered onto the film 412 and patterned byphotolithography. (FIG. 10B). In one embodiment, the film is aluminumbut it could be any metal that can be sputtered onto the film 412. Using413 mask, 412 is etched to substrate in oxygen plasma. (FIG. 10C). Thefilm 412 is patterned so that only the region above the microcavity isopened. In one embodiment, when the device is to be used as a biosensor,the device is incubated in aminopropyldimethysiloxane so that thesilicon dioxide above the photonic crystal microcavity can form aminebonds for binding of biomolecules. Simultaneously, PDMS microfluidicchannels are prepared by molding technique. A master silicon wafer 421,cleaned in Piranha solution and rinsed is dried and subsequently, aphotoresist 422 is spin-coated on the silicon wafer. In one embodiment,the photoresist is SU-8 but it can be any lithographically patternedpolymer that can give high aspect ratio features. After patterning 422(FIG. 10D) and baking, a mixture of another polymer precursor 423 andcuring agent in the ratio of 10:1 volume together with a hydrophilicadditive is poured over the 422 mold, as shown in FIG. 10E. In thisembodiment the polymer 423 is polydimethylsiloxane, popularly known asPDMS. After complete curing, the 423 layers will be removed from themold to achieve the structure as shown in FIG. 10F. The PDMSmicrofluidic channel is carefully aligned and mounted on the structurepatterned in FIG. 10C, as shown in FIG. 10G. Solutions 432 containingdifferent biomolecule samples 431 will be introduced into microchannelsas illustrated in FIG. 10H. Biomolecules will be selectively depositedon exposed sites in each channel on the photonic crystal microcavity.After initial biomolecule deposition, microchannels will be thoroughlywashed with PBS to purge them of any excess, unbound biomolecule and themicrochannels peeled off using tweezers. Finally, the microchannel whilethe device as a whole is maintained in solution 432 as shown in FIG.10I. The final photonic crystal microcavities coupled to waveguidemicroarray device with patterned proteins has been shown schematicallyin FIG. 3.

FIG. 11 is the top view of the device in FIG. 10G and FIG. 10H. Asillustrated, openings in the parylene (412) are lithographically definedso that the photonic crystal microcavity regions of 201 and 202 areexposed. The procedure applies to all microcavities 20 n. The PDMSmicrochannels are depicted by the dotted elements 423. Molecules andtarget biomolecules 431 and 432 corresponding respectively tobiomolecular specific coatings on photonic crystal microcavities 201 and202 are flown in through the microfluidic channels in the direction ofthe arrows. Biomolecules 431 and 432 correspond to 301 and 302respectively in FIG. 3. Since the open areas in 412 have been silanized,biomolecules 301 (431) and 302 (432) preferentially bind to the photoniccrystal substrate above the photonic crystal microcavities 201 and 202respectively. The same principle applies to all N photonic crystalmicrocavities arrayed along the length of the photonic crystal waveguide100. Thus, there is no cross-contamination between 301 (431) and 302(432).

In one embodiment, the slab 101 is formed from a material of highrefractive index including, but not limited to, silicon, germanium,carbon, gallium nitride, gallium arsenide, gallium phosphide, indiumnitride, indium phosphide, indium arsenide, zinc oxide, zinc sulfide,silicon oxide, silicon nitride, alloys thereof, metals, and organicpolymer composites. Single crystalline, polycrystalline, amorphous, andother forms of silicon may be used as appropriate. Organic materialswith embedded inorganic particles, particularly metal particles, may beused to advantage. In one embodiment, the top cladding 106 and bottomcladding 105 are formed from a material whose refractive index is lowerthan that of the slab material. Suitable top cladding and bottomcladding materials include, but not limited to, air, silicon oxide,silicon nitride, alumina, organic polymers and alloys thereof. Thesubstrate 107 materials include, but not limited to, silicon, galliumarsenide, indium phosphide, gallium nitride, sapphire, glass, polymerand alloys thereof. In one embodiment, the columnar members 102 areformed from a material whose refractive index is substantial differentfrom that of the slab 101. Suitable materials for the columnar members102 include, but not limited to, air, silicon oxide, silicon nitride,alumina, organic polymers, or alloys thereof. In one preferredembodiment, the slab 101 is formed from silicon, the columnar members102 are formed from air, the top cladding 106 is air, and the bottomcladding 105 is formed from silicon oxide, while the substrate 107 issilicon.

Although the word “biomolecule” is used in the preceding discussions,one skilled in the art will understand that it refers to a general formof biomolecule that includes, but not limited to, proteins,deoxyribonucleic acid (DNA), ribonucleic acid (RNA), genes, antigens,antibodies, small molecules, nucleic acids, bacteria, viruses and anyarrayed combination thereof for the specific diagnosis of diseases.“Molecule” can denote any polymer or hydrogel that responds to changesin the ambient medium of the device. Any combination of “molecules” and“biomolecules” can be arrayed on the device to get precise knowledge ofprocess conditions, system conditions, analyte identification and/orbinding events for disease identification.

Although the word “light” or “lightwave” is used to denote signals inthe preceding discussions, one skilled in the art will understand thatit refers to a general form of electromagnetic radiation that includes,and is not limited to, visible light, infrared light, ultra-violetlight, radios waves, and microwaves.

In summary, the present invention provides an ultra compact microarraydevice architecture using two-dimensional photonic crystal microcavitiescoupled to a single photonic crystal waveguide, together with a newmicrofluidic technique that preserves the biomolecule functionality inaqueous phase. The invention enables massively parallel, label-free,on-chip multi-analyte sensing for biochemical sensing and a diagnosticassay for any disease, which displays target-probe biomoleculeconjugation. The biomolecule of interest can be DNA, RNA, proteins,nucleic acids and small molecules. It incorporates a new microfluidictechnique with photonic crystal devices, that allows patterning ofbiomolecules in the aqueous phase. Owing to the small dimensions of thedevices presented herein, one can monolithically integrate the photoniccrystal microarrays on silicon VLSI chips. The CMOS compatible photoniccrystal microarray devices have simpler design requirements than themicroelectronics industry. Furthermore, easy regeneration capability andhigh measurement throughput ensures that our miniature compact deviceswill deliver improved results with significantly lower cost to thecustomer. The device is of extreme significance in basic biologicalsciences and human health diagnostics, as well as in the food andbeverage industry and in bio-warfare defense.

While the invention has been described in connection with a number ofpreferred embodiments, it is not intended to limit the scope of theinvention to the particular form set forth, but on the contrary, it isintended to cover such alternatives, modifications, and equivalents asmay be included within the design concept of the invention as defined bythe appended claims.

1. A high throughput diagnostic assay and multiple analyte detectionapparatus for simultaneous diagnosis or detection of multiple species,comprising a photonic crystal waveguide and an array of photonic crystalmicrocavities and further comprising: a substrate; a slab disposed onthe substrate; a plurality of void columnar members etched through theslab, wherein the plurality of void columnar members form a periodiclattice with a lattice constant α; a core in the slab having an inputside on a first end of the photonic crystal waveguide and an output sideon a second end of the photonic crystal waveguide; the photonic crystalwaveguide formed within the core by a row of void columnar members fromthe input side to the output side, wherein the row of void columnarmembers is filled with the material of the slab; an input impedancetaper in the photonic crystal waveguide at the input side of thephotonic crystal waveguide in the plane of the slab, wherein the inputimpedance taper is formed by one or more void columnar members from theinput side shifted away and normal to the photonic crystal waveguide andadjacent the length of both sides of the photonic crystal waveguide; aninput ridge waveguide in the core coupled to the input impedance taperin the photonic crystal waveguide, in the plane of the slab; an outputimpedance taper in the photonic crystal waveguide at the output side ofthe photonic crystal waveguide in the plane of the slab, wherein theoutput impedance taper is formed by one or more void columnar membersfrom the output side shifted away and normal to the photonic crystalwaveguide and adjacent the length of both sides of the photonic crystalwaveguide; and an output ridge waveguide in the core coupled to theoutput impedance taper in the photonic crystal waveguide, in the planeof the slab; wherein the array of photonic crystal microcavitiescomprise one or more optical microcavities formed by a group of columnarmembers, wherein the group of columnar members is filled with thematerial of the slab and wherein the one or more optical microcavitiesare parallel to and shorter than the core are separated from each otherand the photonic crystal waveguide by one or more lattice constants;wherein the photonic crystal waveguide supports one or more guided modesof a broadband source; wherein the array of photonic crystalmicrocavities with one or more polymer molecules or biomolecules coatedon the array of photonic crystal microcavities support one or moreresonance modes comprising one or more resonant frequencies resulting inminima in the transmission spectrum of the one or more guided modes ofthe broadband source at the corresponding resonant frequencies of theone or more optical microcavities; and wherein the one or more polymermolecules or biomolecules bind other molecules resulting in shifting theresonance frequencies of the one or more optical microcavities and hencethe minima in the transmission spectrum of the one or more guided modesof the broadband source.
 2. The apparatus of claim 1, wherein the inputimpedance taper is formed by the first eight void columnar membersshifted from the input end by x times α, where x ranges from 0.4 to 0.05in decrements of 0.05 and wherein the output impedance taper is formedby the first eight void columnar members shifted from the output end byx times α, where x ranges from 0.4 to 0.05 in decrements of 0.05.
 3. Theapparatus of claim 1, wherein the frequencies of the one or more guidedmodes are tuned by changing at least one of: the diameter of the voidcolumnar members, the spacing of the void columnar members, the width ofthe slab, and the thickness of the slab.
 4. The apparatus of claim 1,wherein each of the one or more optical microcavities uniquely supportone or more resonance modes.
 5. The apparatus of claim 1, wherein theone or more resonant frequencies of the one or more resonance modes ofthe one or more optical microcavities are tuned by changing at least oneof: the spacing of the void columnar members adjacent to the one or moreoptical microcavities and the diameter of the void columnar membersadjacent to the one or more optical microcavities.
 6. The apparatus ofclaim 1, wherein the slab material is selected from the group consistingof: silicon, germanium, carbon, gallium nitride, gallium arsenide,gallium phosphide, indium nitride, indium phosphide, aluminum arsenide,zinc oxide, silicon oxide, silicon nitride, alloys thereof, and organicpolymers.
 7. The apparatus of claim 1, wherein the plurality of voidcolumnar members are filled with material selected from the groupconsisting of: air, silicon oxide, silicon nitride, and organicpolymers.
 8. The apparatus of claim 1, wherein each of the one or moreoptical microcavities are coated with different polymer molecules orbiomolecules.
 9. The apparatus of claim 1, wherein one or moremicrofluidic channels are arrayed orthogonal to the photonic crystalwaveguide in the plane of the slab to eliminate cross-contaminationbetween the one or more polymer molecules and biomolecules.
 10. Theapparatus of claim 1, wherein the one or more polymer molecules andbiomolecules are preserved in an aqueous phase to preserve thefunctionality of the one or more polymer molecules and biomolecules. 11.The apparatus of claim 1, wherein the one or more biomolecules areproteins, deoxyribonucleic acid, ribonucleic acid, small molecules,genes, nucleic acids, antigens, or antibodies, each of which shows aspecific response to its specific conjugate antigen in blood, serum,saliva or animal fluid.
 12. The apparatus of claim 1, wherein the one ormore polymer molecules are configured to change refractive index with achange in ambient conditions including but not limited to temperature,pressure, humidity, presence of trace gases (greenhouse andnon-greenhouse), groundwater contaminants (organic/inorganic,volatile/non-volatile), and pesticides.